[STORY] Merge T1 pipeline sections into a single script

[tclose]

Metadata

Epic: #17
Feature: #79
Feature Release:
Required knowledge: shallow or mid-level or deep

Description

As a researcher, I want to have use a single script to do all the T1w image processing

This can be done by combining #247 and #230 along with conditional statements to execute user-specified options

Acceptance Criteria

A workflow written in pydra that is able to execute the following (followed by user-input options)

• FastSurfer (yes or no input options)
• 5TTgen HSVS along with visualisation image (yes or no input options)
• parcellation image (none or parcellation-image label input options)

List of secondary tasks

• move from local usage to usage on XNAT
• expand the catalogue to include parcellations that are not part of Free/FastSurfer (create separate story for this later)

Tasks

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1. provide LUT as an output (for user's benefit)
2. script modifications for BN: change 5tt algorithm from HSVS to FS (since labelsgmfix is not sensible with this atlas), skip labelconver and labelSGMfix
3. use docker container for FS
4. update LUT for HCPMMP1 (use what we did for HCP_cd)

[arkiev]

Decided to execute FastSurfer, fTT and parcellation generation all at once (i.e., single input being T1, all outputs generated)